Glad to see your issue has been solved!
There is a lot to learn about RV electrical systems. I don't have an Expedition, but here are a few pointers about such systems.
There are at least two 12 volt battery systems in an RV and one in a TT. The two are, "Chassis" for the engine and "House" for living area 12 volt power.
Generators sometimes start from chassis and sometimes start from house. It helps if you know which is true for your RV.
Manufacturers often install a "Disconnect" switch in a convenient place to turn most 12 volt house stuff off for storage. As you have discovered it often also turns charging off. However, the manufacturer switch probably leaves some safety and maybe automatic power monitoring systems on. With the batteries fully charged, you may get one to two weeks of storage before recharge is needed. Monitor battery voltage to know when to recharge. Keep them above 12.4 volts for best battery life.
Some owners install a second disconnect switch near the batteries. That one usually completely disconnects the 12 volt house batteries. Starting fully charged and with flooded cell batteries in excellent condition, you can usually store for 6 months before recharging. AGM batteries usually last for 12 months.
Measure the voltage at the battery terminals to know when to recharge. Keep the voltage during storage above 12.4 volts for long useful life. You apparently know it takes a long time to fully charge. Usually it takes 14 to 18 hours to fully clean the sulfate off the battery plates before storage.
As far as damage from drawing the batteries down flat is concerned, deep draw house batteries are resistant to damage. It does cost some life each time flooded cell batteries are excessively discharged. AGM batteries are much more resistant to flat out discharge. You probably won’t notice any difference.
Automotive start batteries are different. Deep or flat out discharge will probably decrease starting capacity and reduce cycle life. It will be most noticeable in cold weather. I don’t mean Florida cold weather. I mean Wisconsin cold weather.
There is a lot more to learn about your RV power systems and battery systems. Ask about what you are interested in.
I wish you good luck and happy trails ahead!